R Observatory: Metrics for ProgModule version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2025-09-20. Its history is shown below.

Reason: requires archived package 'pathwayTMB'

Details below reflect version 0.1.0, its last release before removal.

ProgModule

0.1.0

Identification of Prognosis-Related Mutually Exclusive Modules

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Junwei Han1 releasesCRAN page ↗

A novel tool to identify candidate driver modules for predicting the prognosis of patients by integrating exclusive coverage of mutations with clinical characteristics in cancer.

Install

R (source archive)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/ProgModule/ProgModule_0.1.0.tar.gz"
pkgFile <- "ProgModule_0.1.0.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.1.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-progmodule

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

9

Dependencies · direct

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 25%
Documented parameters: 77%
Return-value docs: 100%
References docs: 0%

Downloads

ProgModule Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on105 r2u

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (9)

igraph infotheo maftools patchwork pathwayTMBstatssurvivalsurvminerutils

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Junwei Han

Author, Maintainer, Copyright holder

Authors (3)

Junwei Han

Author, Maintainer, Copyright holder

Xiangmei Li

Author

Bingyue Pan

Author

Copyright holders (1)

Junwei Han

Author, Maintainer, Copyright holder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-09-20
requires archived package 'pathwayTMB'
R
R 4.5.0 released · 2025-04-11
0.1.0
2024-05-16
R
R 4.4.0 released · 2024-04-24

Package metadata

Total releases: 1
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Bundled data: 136 KB / 11 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ProgModule")

Format

Han, J., Li, X., & Pan, B. (n.d.). ProgModule: Identification of Prognosis-Related Mutually Exclusive Modules (Version 0.1.0) [Computer software]. Retrieved August 15, 2026, from https://CRAN.R-project.org/package=ProgModule

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for ProgModule version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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